NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q04648 UniProt NPD GO	CCBS_OENBE	Probable cytochrome c biosynthesis protein	0.16	-	end	9 *					577
Q9USD4 UniProt NPD GO	ALG12_SCHPO	Probable dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mann ...	0.16	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum [ISS]			546
Q09689 UniProt NPD GO	IF5_SCHPO	Probable eukaryotic translation initiation factor 5 (eIF-5)	0.16	+	nuc	0					395
Q9SIK1 UniProt NPD GO	GLGL4_ARATH	Probable glucose-1-phosphate adenylyltransferase large subunit, chloroplast precursor (EC 2.7.7.27) ...	0.16	-	cyt	0	Plastid; chloroplast				523
Q9SYJ2 UniProt NPD GO	GPAT3_ARATH	Probable glycerol-3-phosphate acyltransferase 3 (EC 2.3.1.15) (AtGPAT3)	0.16	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				520
P34517 UniProt NPD GO	GPDA_CAEEL	Probable glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic (EC 1.1.1.8)	0.16	-	mit	0	Cytoplasm (By similarity)				392
Q6L500 UniProt NPD GO	H2A4_ORYSA	Probable histone H2A.4	0.16	+	nuc	0	Nucleus (By similarity)				163
Q93ZR1 UniProt NPD GO	ELP3_ARATH	Probable histone acetyltransferase ELO3 (EC 2.3.1.48) (Protein ELONGATA 3) (Elongator component 3) ( ...	0.16	-	cyt	0	Nucleus (Probable)				565
P90917 UniProt NPD GO	RBA1_CAEEL	Probable histone-binding protein rba-1	0.16	-	cyt	0	Nucleus (By similarity)				412
Q34807 UniProt NPD GO	IEND1_PICCA	Probable intron-encoded endonuclease 1 (EC 3.1.-.-)	0.16	-	cyt	0	Mitochondrion				231
O94479 UniProt NPD GO	YC6C_SCHPO	Probable metallopeptidase C1919.12c (EC 3.4.-.-)	0.16	-	end	9 *	Membrane; multi-pass membrane protein				843
Q21735 UniProt NPD GO	NTF2_CAEEL	Probable nuclear transport factor 2 (NTF-2)	0.16	-	cyt	0	Cytoplasm (By similarity)				133
Q9M9S2 UniProt NPD GO	PEL3_ARATH	Probable pectate lyase 3 precursor (EC 4.2.2.2) (Pectate lyase A2)	0.16	-	mit	1 *					459
Q5MFV6 UniProt NPD GO	PMEL_ARATH	Probable pectinesterase VGDH2 precursor (EC 3.1.1.11) (Pectin methylesterase) (PE) (VANGUARD1-like p ...	0.16	-	end	1 *					588
Q86Y79 UniProt NPD GO	PTH_HUMAN	Probable peptidyl-tRNA hydrolase (EC 3.1.1.29) (PTH)	0.16	-	mit	0					214
Q19311 UniProt NPD GO	PUR4_CAEEL	Probable phosphoribosylformylglycinamidine synthase (EC 6.3.5.3) (FGAM synthase) (FGAMS) (Formylglyc ...	0.16	-	nuc	0	Cytoplasm (By similarity)				1343
Q8SRW9 UniProt NPD GO	SC61G_ENCCU	Probable protein transport protein SEC61 subunit gamma	0.16	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				72
P11718 UniProt NPD GO	ATXA_LEIDO	Probable proton ATPase 1A (EC 3.6.3.6) (LDH1A protein)	0.16	-	end	8	Membrane; multi-pass membrane protein				974
P12522 UniProt NPD GO	ATXB_LEIDO	Probable proton ATPase 1B (EC 3.6.3.6) (LDH1B protein)	0.16	-	end	8	Membrane; multi-pass membrane protein				974
Q23623 UniProt NPD GO	TGT_CAEEL	Probable queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine transglycosylase) (Guanine inse ...	0.16	-	mit	0					400
O94460 UniProt NPD GO	TGT_SCHPO	Probable queuine tRNA-ribosyltransferase (EC 2.4.2.29) (tRNA-guanine transglycosylase) (Guanine inse ...	0.16	-	mit	0					404
Q09543 UniProt NPD GO	2AAA_CAEEL	Probable serine/threonine-protein phosphatase PP2A regulatory subunit (Protein phosphatase PP2A regu ...	0.16	-	cyt	0					590
P51343 UniProt NPD GO	YCF29_PORPU	Probable transcriptional regulator ycf29	0.16	-	cyt	0	Plastid; chloroplast				209
Q9C0V8 UniProt NPD GO	YHJ1_SCHPO	Probable transporter PB10D8.01	0.16	-	end	10	Membrane; multi-pass membrane protein				552
O74468 UniProt NPD GO	SUMT_SCHPO	Probable uroporphyrin-III C-methyltransferase (EC 2.1.1.107)	0.16	-	cyt	0					496
Q39857 UniProt NPD GO	XTH_SOYBN	Probable xyloglucan endotransglucosylase/hydrolase precursor (EC 2.4.1.207) (Fragment)	0.16	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				295
P51924 UniProt NPD GO	GON2A_CARAU	Progonadoliberin IIA precursor [Contains: Gonadoliberin II (Luteinizing hormone-releasing hormone II ...	0.16	-	exc	1 *	Secreted protein				86
Q15116 UniProt NPD GO	PDCD1_HUMAN	Programmed cell death protein 1 precursor (Protein PD-1) (hPD-1) (CD279 antigen)	0.16	-	nuc	1	Membrane; single-pass type I membrane protein		600244		288
Q9JKL1 UniProt NPD GO	PKR1_MOUSE	Prokineticin receptor 1 (PK-R1) (G-protein coupled receptor 73)	0.16	-	end	7	Membrane; multi-pass membrane protein				393
P18918 UniProt NPD GO	PLF3_MOUSE	Proliferin-3 precursor (Mitogen-regulated protein 3)	0.16	-	mit	0	Secreted protein				224
O15460 UniProt NPD GO	P4HA2_HUMAN	Prolyl 4-hydroxylase alpha-2 subunit precursor (EC 1.14.11.2) (4-PH alpha-2) (Procollagen-proline,2- ...	0.16	-	vac	0	Endoplasmic reticulum; endoplasmic reticulum lumen		600608		535
P43253 UniProt NPD GO	PI2R_RAT	Prostacyclin receptor (Prostanoid IP receptor) (PGI receptor) (Prostaglandin I2 receptor)	0.16	-	end	6 *	Membrane; multi-pass membrane protein				416
Q5XIU5 UniProt NPD GO	PSMF1_RAT	Proteasome inhibitor PI31 subunit	0.16	-	nuc	0					271
P52428 UniProt NPD GO	PSA1_ORYSA	Proteasome subunit alpha type 1 (EC 3.4.25.1) (20S proteasome alpha subunit F) (20S proteasome subun ...	0.16	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				270
P34119 UniProt NPD GO	PSA4_DICDI	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome component DD4)	0.16	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
P28063 UniProt NPD GO	PSB8_MOUSE	Proteasome subunit beta type 8 precursor (EC 3.4.25.1) (Proteasome component C13) (Macropain subunit ...	0.16	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				276
Q43495 UniProt NPD GO	108_LYCES	Protein 108 precursor	0.16	-	exc	1 *					102
Q9LV66 UniProt NPD GO	Y5848_ARATH	Protein At5g48480	0.16	-	cyt	0				1XY7	166
Q6P7Q1 UniProt NPD GO	BRE_RAT	Protein BRE (Brain and reproductive organ-expressed protein)	0.16	-	cyt	0	Cytoplasm; cytosol (By similarity). Mainly. Nucleus (By similarity). Also nuclear	cytoplasm [ISS] nuclear ubiquitin ligase complex [ISS] nucleus [ISS]			383
Q6AXX6 UniProt NPD GO	CJ058_RAT	Protein C10orf58 homolog precursor	0.16	-	mit	1 *	Secreted protein (Potential)				229
Q9CQF4 UniProt NPD GO	CF203_MOUSE	Protein C6orf203 homolog	0.16	-	nuc	0					240
Q96L11 UniProt NPD GO	CG034_HUMAN	Protein C7orf34 precursor (MSSP-binding protein CTM-1)	0.16	-	end	0					122
Q9NRH1 UniProt NPD GO	CG036_HUMAN	Protein C7orf36	0.16	-	nuc	0					226
Q60HH0 UniProt NPD GO	CLN3_MACFA	Protein CLN3 (Battenin)	0.16	-	end	8 *	Lysosome; lysosomal membrane; multi-pass membrane protein (By similarity)				438
Q96IK1 UniProt NPD GO	FA44B_HUMAN	Protein FAM44B	0.16	-	nuc	0					185
Q99339 UniProt NPD GO	GIN11_YEAST	Protein GIN11	0.16	-	nuc	0					116
O77049 UniProt NPD GO	JTB_BRUMA	Protein JTB precursor	0.16	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				146
P53990 UniProt NPD GO	K0174_HUMAN	Protein KIAA0174 (Putative MAPK-activating protein PM28)	0.16	-	nuc	0		ER-Golgi intermediate compartment [IDA]			364
P54815 UniProt NPD GO	MSP1_CAEEL	Protein MSP1 homolog	0.16	-	mit	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				342
Q4IBD0 UniProt NPD GO	PBN1_GIBZE	Protein PBN1	0.16	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...				488

You are viewing entries 56101 to 56150 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.